src/inc/bigBed.h 1.14

Index: src/inc/bigBed.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/inc/bigBed.h,v
retrieving revision 1.13
retrieving revision 1.14
diff -b -B -U 1000000 -r1.13 -r1.14
--- src/inc/bigBed.h	29 Apr 2009 17:59:33 -0000	1.13
+++ src/inc/bigBed.h	13 May 2009 01:13:57 -0000	1.14
@@ -1,125 +1,97 @@
 /* bigBed - interface to binary file with bed-style values (that is a bunch of
  * possibly overlapping regions.
  *
  * This shares a lot with the bigWig module. */
 
 #ifndef BIGBED_H
 #define BIGBED_H
 
 #ifndef BBIFILE
 #include "bbiFile.h"
 #endif
 
 struct bigBedInterval
 /* A partially parsed out bed record plus some extra fields. */
     {
     struct bigBedInterval *next;	/* Next in list. */
     bits32 start, end;		/* Range inside chromosome - half open zero based. */
     char *rest;			/* Rest of line. May be NULL*/
     };
 
 struct ppBed
 /* A partially parsed out bed record plus some extra fields. */
     {
     struct ppBed *next;	/* Next in list. */
     char *chrom;		/* Chromosome name (not allocated here) */
     bits32 start, end;		/* Range inside chromosome - half open zero based. */
     char *rest;			/* The rest of the bed. */
     bits64 fileOffset;		/* File offset. */
     bits32 chromId;		/* Chromosome ID. */
     };
 
 struct bbiFile *bigBedFileOpen(char *fileName);
 /* Open up big bed file.   Free this up with bbiFileFree */
 
 struct bigBedInterval *bigBedIntervalQuery(struct bbiFile *bbi, char *chrom, 
 	bits32 start, bits32 end, int maxItems, struct lm *lm);
 /* Get data for interval.  Return list allocated out of lm.  Set maxItems to maximum
  * number of items to return, or to 0 for all items. */
 
 int bigBedIntervalToRow(struct bigBedInterval *interval, char *chrom, char *startBuf, char *endBuf,
 	char **row, int rowSize);
 /* Convert bigBedInterval into an array of chars equivalent to what you'd get by
  * parsing the bed file. The startBuf and endBuf are used to hold the ascii representation of
  * start and end.  Note that the interval->rest string will have zeroes inserted as a side effect. 
  * Returns number of fields in row.  */
 
 boolean bigBedSummaryArray(struct bbiFile *bbi, char *chrom, bits32 start, bits32 end,
 	enum bbiSummaryType summaryType, int summarySize, double *summaryValues);
 /* Fill in summaryValues with  data from indicated chromosome range in bigBed file.
  * Be sure to initialize summaryValues to a default value, which will not be touched
  * for regions without data in file.  (Generally you want the default value to either
  * be 0.0 or nan("") depending on the application.)  Returns FALSE if no data
  * at that position. */
 
 boolean bigBedSummaryArrayExtended(struct bbiFile *bbi, char *chrom, bits32 start, bits32 end,
 	int summarySize, struct bbiSummaryElement *summary);
 /* Get extended summary information for summarySize evenely spaced elements into
  * the summary array. */
 
 bits64 bigBedItemCount(struct bbiFile *bbi);
 /* Return total items in file. */
 
 struct asObject *bigBedAs(struct bbiFile *bbi);
 /* Get autoSql object definition if any associated with file. */
 
 void bigBedFileCreate(
 	char *inName, 	  /* Input file in a tabular bed format <chrom><start><end> + whatever. */
 	char *chromSizes, /* Two column tab-separated file: <chromosome> <size>. */
 	int blockSize,	  /* Number of items to bundle in r-tree.  1024 is good. */
 	int itemsPerSlot, /* Number of items in lowest level of tree.  64 is good. */
 	bits16 definedFieldCount,  /* Number of defined bed fields - 3-16 or so.  0 means all fields
 				    * are the defined bed ones. */
 	char *asFileName, /* If non-null points to a .as file that describes fields. */
+	boolean clip,     /* If set silently clip out of bound coordinates. */
 	char *outName);   /* BigBed output file name. */
 /* Convert tab-separated bed file to binary indexed, zoomed bigBed version. */
 
-void bigBedFileCreateReadInfile(
-	char *inName, 	  /* Input file in a tabular bed format <chrom><start><end> + whatever. */
-	char *chromSizes, /* Two column tab-separated file: <chromosome> <size>. */
-	int blockSize,	  /* Number of items to bundle in r-tree.  1024 is good. */
-	int itemsPerSlot, /* Number of items in lowest level of tree.  64 is good. */
-	bits16 definedFieldCount,  /* Number of defined bed fields - 3-16 or so.  0 means all fields
-				    * are the defined bed ones. */
-	char *asFileName, /* If non-null points to a .as file that describes fields. */
-	char *outName,    /* BigBed output file name. */
-	struct ppBed **ppbList,   /* Input bed data, will be sorted. */
-	bits64 *count,            /* size of input pbList */
-	double *averageSize,      /* average size of elements in pbList */
-	struct hash **pChromHash,  /* Hash containing sizes of all chroms. */
-	bits16 *fieldCount,       /* actual field count from input data. */
-	struct asObject **pAs,    /* If non-null contains as object that describes fields. */
-	bits64 *fullSize);         /* full size of ppBed on disk */
-/* Load data to prepare bigBed. */
-
 void bigBedFileCreateDetailed(
 	struct ppBed *pbList, 	  /* Input bed data. Must be sorted. */
 	bits64 pbCount,           /* size of input pbList */
 	double pbAverageSize,     /* average size of elements in pbList */
 	char *inName,             /* Input file name (for error message reporting) */
 	struct hash *chromHash,   /* Hash containing sizes of all chroms. */
 	int blockSize,	  /* Number of items to bundle in r-tree.  1024 is good. */
 	int itemsPerSlot, /* Number of items in lowest level of tree.  64 is good. */
 	bits16 definedFieldCount, /* Number of defined bed fields - 3-16 or so.  0 means all fields
 				    * are the defined bed ones. */
 	bits16 fieldCount,        /* actual field count from input data. */
 	char *asFileName,         /* If non-null points to a .as file that describes fields. */
 	struct asObject *as,      /* If non-null contains as object that describes fields. */
 	bits64 fullSize,          /* full size of ppBed on disk */
 	char *outName);            /* BigBed output file name. */
 /* create zoomed bigBed version from ppBed list. */
 
-struct ppBed *ppBedLoadOne(char **row, int fieldCount, struct lineFile *lf, struct hash *chromHash, struct lm *lm, struct asObject *as, bits64 *diskSize);
-/* Return a ppBed record from a line of bed file in lf.
-   Return the disk size it would occupy in *diskSize.
-   row is a preallocated array of pointers to the individual fields in this row to load.
-   fieldCount is the number of fields.
-   lf is the lineFile the row is coming from, used for error messages and parsing fields.
-   chromHash is a hash of the chromosome sizes.
-   lm is localMem to allocate ppBed memory from - don't ppBedFreeList or slFree
-   list!
-   as is the autoSql object describing this bed file or NULL if standard bed.
-   */
 
 #endif /* BIGBED_H */